Analysis of the algorithm: From rankings to backup genes.
Ranking section
Table 1. Performance summary for every kernel and net before integration.
| Net | Kernel | tpr_down_ci_0.95 | tpr_up_ci_0.95 | fpr_down_ci_0.95 | fpr_up_ci_0.95 | f |
|---|---|---|---|---|---|---|
| biological_process | ct | 1 | 1 | 1 | 1 | 0.958333333333333 |
| biological_process | el | 1 | 1 | 1 | 1 | 0.958333333333333 |
| biological_process | ka | 1 | 1 | 1 | 1 | 0.958333333333333 |
| biological_process | rf | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | ct | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | el | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | ka | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | node2vec | 1 | 1 | 1 | 1 | 0.958333333333333 |
| disease | rf | 1 | 1 | 1 | 1 | 0.958333333333333 |
| genetic_interaction_weighted | ct | 0.819444444444444 | 1 | 0.5 | 1 | 0.966442953020134 |
| genetic_interaction_weighted | el | 1 | 1 | 0.666666666666667 | 1 | 0.96 |
| genetic_interaction_weighted | ka | 1 | 1 | 1 | 1 | 0.96 |
| genetic_interaction_weighted | rf | 0.819444444444444 | 1 | 0.5 | 1 | 0.966442953020134 |
| molecular_function | ct | 1 | 1 | 1 | 1 | 0.923076923076923 |
| molecular_function | el | 1 | 1 | 0 | 1 | 0.923076923076923 |
| molecular_function | ka | 1 | 1 | 0 | 1 | 0.923076923076923 |
| molecular_function | node2vec | 1 | 1 | 0 | 0 | 1 |
| molecular_function | rf | 1 | 1 | 0 | 1 | 0.923076923076923 |
| pathway | ct | 0.551724137931034 | 1 | 0.333333333333333 | 1 | 0.918032786885246 |
| pathway | el | 0.448275862068966 | 1 | 0.166666666666667 | 1 | 0.935483870967742 |
| pathway | ka | 1 | 1 | 1 | 1 | 0.90625 |
| pathway | node2vec | 1 | 1 | 0.5 | 1 | 0.90625 |
| pathway | rf | 0.481896551724139 | 1 | 0.166666666666667 | 1 | 0.935483870967742 |
| phenotype | ct | 1 | 1 | 0 | 1 | 0.956521739130435 |
| phenotype | el | 1 | 1 | 0 | 1 | 0.956521739130435 |
| phenotype | ka | 1 | 1 | 1 | 1 | 0.956521739130435 |
| phenotype | node2vec | 1 | 1 | 0.5 | 1 | 0.956521739130435 |
| phenotype | rf | 1 | 1 | 0.487500000000011 | 1 | 0.956521739130435 |
| protein_interaction | ct | 0.902777777777778 | 1 | 0.166666666666667 | 1 | 0.972602739726027 |
| protein_interaction | el | 0.847222222222222 | 1 | 0.166666666666667 | 1 | 0.972602739726027 |
| protein_interaction | ka | 1 | 1 | 0.833333333333333 | 1 | 0.96 |
| protein_interaction | node2vec | 0.860763888888889 | 1 | 0.333333333333333 | 1 | 0.972972972972973 |
| protein_interaction | rf | 0.888888888888889 | 1 | 0.166666666666667 | 1 | 0.972602739726027 |
Table 2. Performance summary for every kernel after integration
| Integration | Kernel | tpr_down_ci_0.95 | tpr_up_ci_0.95 | fpr_down_ci_0.95 | fpr_up_ci_0.95 | f |
|---|---|---|---|---|---|---|
| integration_mean_by_presence | ct | 1 | 1 | 0.666666666666667 | 1 | 0.96 |
| integration_mean_by_presence | el | 1 | 1 | 0.5 | 1 | 0.96 |
| integration_mean_by_presence | ka | 0.638888888888889 | 0.986111111111111 | 0 | 1 | 0.965034965034965 |
| integration_mean_by_presence | node2vec | 1 | 1 | 1 | 1 | 0.96 |
| integration_mean_by_presence | rf | 0.611111111111111 | 1 | 0.5 | 1 | 0.966442953020134 |
| mean | ct | 1 | 1 | 0.666666666666667 | 1 | 0.96 |
| mean | el | 1 | 1 | 1 | 1 | 0.96 |
| mean | ka | 0.333333333333333 | 1 | 0 | 1 | 0.972222222222222 |
| mean | node2vec | 1 | 1 | 1 | 1 | 0.96 |
| mean | rf | 1 | 1 | 1 | 1 | 0.96 |
Backup Pairs Coverage By Layer
Distribution of ranks in dataset by non integrated kernels
Distribution of ranks in dataset by Integrated kernels
ROC-AUCs for Non-integrated kernel and layer
ROC-AUCS for integrated kernels
CDF plots of non integrated kernels
ROC plots of non integrated kernels
ROC plots of integrated kernels
CDF plots of integrated kernels